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Sodium in PDB 5jea: Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna

Enzymatic activity of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna

All present enzymatic activity of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna:
3.2.1.17;

Protein crystallography data

The structure of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna, PDB code: 5jea was solved by E.Kowalinski, J.Ebert, E.Stegmann, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.69 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.080, 182.530, 250.550, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 25.9

Other elements in 5jea:

The structure of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna (pdb code 5jea). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna, PDB code: 5jea:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5jea

Go back to Sodium Binding Sites List in 5jea
Sodium binding site 1 out of 4 in the Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:58.0
occ:1.00
 OG B:SER159 2.5 64.5 1.0
O B:VAL189 2.7 45.7 1.0
O B:GLY191 2.7 47.4 1.0
N B:SER159 3.0 60.9 1.0
N B:GLY191 3.0 58.2 1.0
CB B:SER159 3.1 46.4 1.0
CA B:GLY191 3.4 47.2 1.0
C B:GLY191 3.4 58.0 1.0
C B:VAL189 3.7 49.0 1.0
CA B:SER159 3.7 45.9 1.0
C B:VAL190 3.8 60.3 1.0
O B:TYR157 3.8 46.1 1.0
C B:ILE158 3.9 45.5 1.0
CG B:ARG225 3.9 48.0 1.0
CA B:ILE158 4.0 45.5 1.0
CB B:ARG225 4.1 48.0 1.0
C B:TYR157 4.1 46.1 1.0
N B:ILE158 4.2 45.8 1.0
CB B:TYR157 4.2 49.1 1.0
CA B:VAL190 4.3 57.4 1.0
N B:VAL190 4.3 45.7 1.0
CD B:ARG225 4.3 49.9 1.0
CB B:VAL189 4.5 45.9 1.0
O B:VAL190 4.5 46.7 1.0
CA B:VAL189 4.6 45.9 1.0
CG1 B:VAL189 4.6 46.3 1.0
C B:SER159 4.8 45.5 1.0
N B:LYS192 4.8 54.4 1.0
O B:SER159 4.8 45.4 1.0
CA B:TYR157 4.8 46.6 1.0
O B:ALA221 4.8 59.1 1.0
O B:ILE158 4.9 45.5 1.0

Sodium binding site 2 out of 4 in 5jea

Go back to Sodium Binding Sites List in 5jea
Sodium binding site 2 out of 4 in the Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:64.0
occ:1.00
 O B:ASN20 3.3 53.0 1.0
CD2 B:LEU172 4.4 48.2 1.0
C B:ASN20 4.5 49.6 1.0
CD1 B:ILE216 4.8 48.8 1.0
CA B:GLY220 4.8 55.2 1.0
CB B:ARG223 5.0 61.8 1.0
CB B:ASN20 5.0 61.3 1.0

Sodium binding site 3 out of 4 in 5jea

Go back to Sodium Binding Sites List in 5jea
Sodium binding site 3 out of 4 in the Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na301

b:84.8
occ:1.00
 OG1 F:THR88 2.4 69.5 1.0
O F:GLN90 2.4 51.0 1.0
O F:SER133 2.5 51.3 1.0
N F:SER133 2.8 59.2 1.0
CD1 F:ILE83 2.9 0.7 1.0
OG1 F:THR92 3.0 69.7 1.0
C F:SER133 3.3 50.0 1.0
N F:THR92 3.4 50.8 1.0
C F:GLN90 3.5 52.7 1.0
CB F:THR88 3.5 75.5 1.0
CA F:SER133 3.6 50.0 1.0
C F:GLY91 3.6 51.3 1.0
CA F:GLY91 3.6 51.7 1.0
C F:LYS132 3.8 54.9 1.0
N F:LYS132 3.8 55.5 1.0
CB F:THR92 3.8 65.9 1.0
CA F:LYS132 3.9 53.5 1.0
O F:TYR130 3.9 55.2 1.0
N F:GLY91 4.0 57.6 1.0
CG1 F:ILE83 4.1 86.0 1.0
CA F:THR92 4.2 50.4 1.0
CG2 F:THR88 4.2 69.0 1.0
C F:PRO131 4.3 60.5 1.0
O F:GLY91 4.4 56.4 1.0
N F:GLY134 4.4 49.7 1.0
CB F:SER133 4.6 50.7 1.0
O F:THR88 4.7 64.8 1.0
CA F:THR88 4.8 70.1 1.0
CA F:GLN90 4.8 52.1 1.0
O F:LYS132 4.8 62.2 1.0
N F:GLN90 4.9 51.7 1.0
CA F:PRO131 4.9 53.4 1.0
C F:THR88 4.9 70.6 1.0
O F:PRO131 4.9 51.0 1.0
CA F:GLY134 4.9 49.7 1.0

Sodium binding site 4 out of 4 in 5jea

Go back to Sodium Binding Sites List in 5jea
Sodium binding site 4 out of 4 in the Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex Including SKI7, Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na1103

b:67.9
occ:1.00
 CE J:MET606 3.8 0.4 1.0
N J:MET606 3.8 64.8 1.0
CD2 J:PHE495 3.9 69.0 1.0
CG J:MET606 4.1 82.9 1.0
CA J:PRO605 4.3 74.3 1.0
CE2 J:PHE495 4.3 68.3 1.0
CB J:MET606 4.3 63.0 1.0
CB J:PRO605 4.6 61.6 1.0
C J:PRO605 4.6 74.2 1.0
SD J:MET606 4.7 0.3 1.0
CA J:MET606 4.7 62.0 1.0
CD2 J:LEU500 5.0 63.9 1.0

Reference:

E.Kowalinski, A.Kogel, J.Ebert, P.Reichelt, E.Stegmann, B.Habermann, E.Conti. Structure of A Cytoplasmic 11-Subunit Rna Exosome Complex. Mol.Cell V. 63 125 2016.
ISSN: ISSN 1097-2765
PubMed: 27345150
DOI: 10.1016/J.MOLCEL.2016.05.028
Page generated: Mon Oct 7 21:52:53 2024

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